Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1019 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg1215967035 sf1215964331 12 15967035 3.34E-31 4.33E-19
vg1212877317 sf1212874656 12 12877317 8.80E-18 6.75E-08
vg1203243070 sf1203242073 12 3243070 2.39E-13 NA
vg1218663003 sf1218634438 12 18663003 2.98E-13 9.31E-09
vg1110282765 sf1110277342 11 10282765 4.78E-13 1.59E-06
vg1006587700 sf1006603323 10 6587700 1.32E-12 3.29E-08
vg1011512046 sf1011440865 10 11512046 2.46E-11 5.16E-08
vg1211633613 sf1211630949 12 11633613 4.85E-11 2.01E-07
vg1022588644 sf1022517118 10 22588644 4.67E-10 3.16E-08
vg0809365446 sf0809364450 8 9365446 2.35E-08 3.73E-06
vg1216138955 sf1216136251 12 16138955 NA 3.98E-10
vg1213186520 sf1213183858 12 13186520 NA 4.06E-06
vg0715496678 sf0715495685 7 15496678 NA 4.50E-06